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MicrobeTracker specifications

Information


Unique identifier OMICS_26046
Name MicrobeTracker
Alternative name MicrobeTracker Suite
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB
License GNU General Public License version 3.0
Computer skills Medium
Stability Stable
Registration required Yes
Maintained Yes

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Maintainers


  • person_outline Christine Jacobs-Wagner <>
  • person_outline Thierry Emonet <>

Publication for MicrobeTracker

MicrobeTracker in pipelines

 (2)
2017
PMCID: 5320674
PMID: 28222723
DOI: 10.1186/s12915-017-0348-8

[…] functions and their effects were combined with diffraction-limited imaging to achieve generational tracking and superior cell-division classification using objectj [, ]. another software package, microbetracker, enabled segmentation of cells within a dense population []; microbetracker and its successor oufti [] were recently used to investigate the relationships among growth rate, […]

2017
PMCID: 5379763
PMID: 28376782
DOI: 10.1186/s12918-017-0399-z

[…] discipline in bioinformatics and computer vision []. for bacterial image processing, well known open source software packages for analyzing cell movies are the tlm-tracker [], celltracer [], microbetracker [] and its successor oufti [], and schnitzcells []. the tlm-tracker [] uses multiple alternative algorithms for cell segmentation, such as threshold-based, watershed transform […]


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MicrobeTracker in publications

 (81)
PMCID: 5954120
PMID: 29765094
DOI: 10.1038/s41598-018-25882-y

[…] igg in pbs-triton-bsa. following washing, slides were mounted with 5% (wt/vol) polyvinyl alcohol., images were acquired using the volocity software package. image analysis was performed using the microbetracker matlab software. distributions of cell dimensions among cell populations were represented with box plots displaying the interquartile range (25th and 75th percentiles), the median […]

PMCID: 5910403
PMID: 29679003
DOI: 10.1038/s41467-018-03790-z

[…] raw videos (nd2 format) were converted into tif files using bio-formats plugin, flattened with excitation beam profile as described previously. cell outlines were drawn in microbetracker. for quantification of binding events, peaks were detected in the reactivation phase (fig. : frames 31−50, fig. : frames 51−100, table  and fig. : frames 101−200). peaks were detected […]

PMCID: 5792023
PMID: 29351274
DOI: 10.1371/journal.pgen.1007161

[…] 50 μl/min., we selected regions of images occupied by cells to obtain information about pol iv upregulation upon ciprofloxacin treatment (>200 cells; all 5 min frames during the 3h experiment). microbetracker 0.937 [], a matlab script, was used to create cell outlines as regions of interest (roi). we manually curated cell outlines designated by microbetracker to ensure accuracy […]

PMCID: 5812716
PMID: 29323635
DOI: 10.7554/eLife.31522.039

[…] from1 ml of culture were taken, centrifuged, placed on agarose pad and imaged. as a control, strain carrying empty pbad24 vector was analysed. cells were segmented from brightfield images using microbetracker (). mukb foci were detected using ‘spotfinderm’, available as part of the microbetracker suite., fcs was carried out on a confocor 2 system (carl zeiss). the 633 nm line of a hene […]

PMCID: 5736177
PMID: 29257832
DOI: 10.1371/journal.pbio.2004303

[…] objective (plan-achromat 40×/0.65 ph2; carl zeiss). images were acquired with zen 2 (blue edition; carl zeiss). exposure times and image scaling were identical for compared conditions. microbetracker [] was used to obtain cell outlines. quantitative analysis from cell meshes was done with matlab r2014a (mathworks, inc.) using custom scripts to plot the distributions […]


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MicrobeTracker institution(s)
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT, USA; Department of Physics, Yale University, New Haven, CT, USA; Section of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
MicrobeTracker funding source(s)
Supported by the National Institutes of Health (GM076698 and GM065835), and the National Science Foundation (CCF-0829836).

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